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minfi_getsnp.xml |
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| diff -r 5cab527307f9 -r eb5eccc12a4e minfi_getsnp.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/minfi_getsnp.xml Fri Feb 22 11:13:17 2019 -0500 |
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| @@ -0,0 +1,44 @@ +<tool id="minfi_getsnp" name="Minfi Get SNP" version="@MINFI_VERSION@"> + <description>retrieve the chromosome and the position of each SNP</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"> + <requirement type="package" version="0.6.0">bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19</requirement> + </expand> + <command detect_errors="exit_code"> + <![CDATA[ + Rscript '$minfi_snp_script' + ]]> + </command> + <configfiles> + <configfile name="minfi_snp_script"><![CDATA[ +require("minfi", quietly = TRUE) + +GRSet <- get(load('$grset')) + +snps <- getSnpInfo(GRSet) + +write.table(snps, '$table') + ]]> + </configfile> + </configfiles> +<inputs> + <param type="data" name="grset" format="rdata" label="Genomic Ratio Set" help="This class holds preprocessed data for Illumina methylation microarrays, mapped to a genomic +location."/> + </inputs> + <outputs> + <data name="table" format="txt" label="SNPInfo Table"/> + </outputs> + <tests> + <test> + <param name="grset" value="GRSet.rdata"/> + <output name="table" file="SNPInfo_Table.txt"/> + </test> + </tests> + <help><![CDATA[ + This tool is a version of the getSnpInfo adapted to retrieve the chromosome and the position of each SNP on a given Affymetrix SNP Array. + ]]></help> + <expand macro="citations" /> +</tool> + |